Is ABLIM1 p.Val331Ile (c.991G>A) pathogenic?

ABLIM1 p.Val331Ile (c.991G>A) is classified Uncertain significance in ABLIM1 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-08-13). AlphaMissense: likely benign (0.3349); Ultra-rare (popmax 0.0446%, eas).

How common is ABLIM1 p.Val331Ile (c.991G>A) in the general population?

ABLIM1 p.Val331Ile (c.991G>A) is ultra-rare (popmax 0.0446%, eas) (gnomAD).

What do computational predictors say about ABLIM1 p.Val331Ile (c.991G>A)?

AlphaMissense predicts likely benign (score 0.3349) — an in-silico prediction, not a clinical call.

ABLIM1 p.Val331Ile

c.991G>A · rs200728197 · VCV2365309

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.3349 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0446%, eas)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.3349	likely benign
REVEL	0.139	moderately benign-leaning
SaProt	LLR -5.64	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.7	GERP 2.4, phastCons 1
Regional constraint	o/e 0.75	unconstrained · MANE · 124 kb · p 2.2e-08 · regional, not allelic
Overall
CADD	25.9	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0446% East Asian · 20/44,878 alleles

Filtering AF 0.0295% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0246%

Overall 0.00353% 57/1,614,110 alleles · ultra-rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.0446%	2,244
South Asian	0.00988%	10,118
Admixed American	0.00333%	30,008
European (non-Finnish)	0.00212%	47,201
African / African-American	0.00133%	75,008

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: ABLIM1
Protein: p.Val331Ile
Coding: c.991G>A
MANE Select: NM_002313
dbSNP: rs200728197
Type: single nucleotide variant
Location: chr10:114488008 (GRCh38)
Gene constraint: LOEUF 0.515 · pLI 0.70 (gnomAD)
Structure: AlphaFold pLDDT 59.86
Residue 331: the lim zinc-binding 4 domain

Full ABLIM1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

ABLIM1 p.Ala506Thr Uncertain significance ★★ ⚠ same type
ABLIM1 c.2060-2A>G Uncertain significance ★ same type
ABLIM1 c.379+1G>A Uncertain significance ★ same type
ABLIM1 p.Ala29Val Uncertain significance ★ ⚠ same type
ABLIM1 p.Ala51Thr Uncertain significance ★ ⚠ same type
ABLIM1 p.Ala55Gly Uncertain significance ★ ⚠ same type
ABLIM1 p.Ala83Val Uncertain significance ★ ⚠ same type
ABLIM1 p.Arg112Gln Uncertain significance ★ ⚠ same type

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/ablim1-p-val331ile (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown